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Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies,...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294560/ https://www.ncbi.nlm.nih.gov/pubmed/30215776 http://dx.doi.org/10.1093/nar/gky818 |
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author | Jurisic, Anamarija Robin, Chloé Tarlykov, Pavel Siggens, Lee Schoell, Brigitte Jauch, Anna Ekwall, Karl Sørensen, Claus Storgaard Lipinski, Marc Shoaib, Muhammad Ogryzko, Vasily |
author_facet | Jurisic, Anamarija Robin, Chloé Tarlykov, Pavel Siggens, Lee Schoell, Brigitte Jauch, Anna Ekwall, Karl Sørensen, Claus Storgaard Lipinski, Marc Shoaib, Muhammad Ogryzko, Vasily |
author_sort | Jurisic, Anamarija |
collection | PubMed |
description | Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions. |
format | Online Article Text |
id | pubmed-6294560 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-62945602018-12-21 Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains Jurisic, Anamarija Robin, Chloé Tarlykov, Pavel Siggens, Lee Schoell, Brigitte Jauch, Anna Ekwall, Karl Sørensen, Claus Storgaard Lipinski, Marc Shoaib, Muhammad Ogryzko, Vasily Nucleic Acids Res Methods Online Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions. Oxford University Press 2018-12-14 2018-09-12 /pmc/articles/PMC6294560/ /pubmed/30215776 http://dx.doi.org/10.1093/nar/gky818 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Jurisic, Anamarija Robin, Chloé Tarlykov, Pavel Siggens, Lee Schoell, Brigitte Jauch, Anna Ekwall, Karl Sørensen, Claus Storgaard Lipinski, Marc Shoaib, Muhammad Ogryzko, Vasily Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title | Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title_full | Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title_fullStr | Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title_full_unstemmed | Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title_short | Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
title_sort | topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294560/ https://www.ncbi.nlm.nih.gov/pubmed/30215776 http://dx.doi.org/10.1093/nar/gky818 |
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